fill.contamination: calculate the signature score of one potential contaminated...

In Japrin/scPip: pipeline for scRNA-seq data analysis

calculate the signature score of one potential contaminated cell types (simple average-threshold method)

Description

calculate the signature score of one potential contaminated cell types (simple average-threshold method)

Usage

fill.contamination(
  obj,
  out.prefix,
  assay.name = "norm_exprs",
  g.name = "plasmaB",
  g.test = c("CD79A", "JCHAIN", "SDC1"),
  score.t = 0.75,
  vis.v = c(0.25, 0.5, 0.75, 1)
)

Arguments

obj	object of SingleCellExperiment or Seurat
out.prefix	character; output prefix. (default: NULL)
assay.name	character vector; which assay to use. (default: "norm_exprs").
g.name	character; signature name of the cell type. (default: "plasmaB").
g.test	character vector; signature genes of the cell type. (default: c("CD79A", "JCHAIN", "SDC1")).
score.t	double; threshold for signature score (mean of g.test). (default: 1)
vis.v	double vector; for vertical lines in visulization. (default: c(0.25,0.5,1)).

Details

Two columns will be added to the obj, "

Value

an object of SingleCellExperiment or Seurat

Japrin/scPip documentation built on Jan. 29, 2024, 1:20 a.m.